{ "bcoid": "GLY_000253", "title": "Rat Protein Citations (UniProtKB)", "description": "The Rat Protein Citations dataset contains publication information for rat [taxid:10116] UniProtKB accessions ...", "filename": "rat_protein_citations_uniprotkb.csv", "filetype": "csv", "categories": { "species": "Rattus norvegicus", "molecule": "Protein", "tags": "Protein Citations", "file_type": "csv", "status": "Reviewed", "scope": "internal" }, "minitable": { "content": [ [ "D3ZB48-1...", "Quantitative..." ], [ "P11980-1...", "Quantitative..." ] ], "headers": [ "uniprotkb_ca...", "title..." ], "colwidth": [ "40%", "20%" ] }, "sampledata": { "type": "table", "data": [ [ { "type": "string", "label": "uniprotkb_canonical_ac" }, { "type": "string", "label": "title" }, { "type": "string", "label": "journal_name" }, { "type": "string", "label": "publication_date" }, { "type": "string", "label": "authors" }, { "type": "string", "label": "xref_key" }, { "type": "string", "label": "xref_id" }, { "type": "string", "label": "src_xref_key" }, { "type": "string", "label": "src_xref_id" } ], [ "D3ZB48-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "D3ZB48" ], [ "P11980-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A0G2JVG3" ], [ "Q5M9G6-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q5M9G6" ], [ "Q07969-1", "Luminal lipid regulates CD36 levels and downstream signaling to stimulate chylomicron synthesis.", "J. Biol. Chem.", "2011", "Abumrad N.A., Besnard P., Clement L., Degrace P., Glatz J.F., Monnot M.C., Nassir F., Niot I., Pelsers M.M., Petit V., Poirier H., Tran T.T.", "protein_xref_pubmed", "21610069", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "CD36 involvement in orosensory detection of dietary lipids, spontaneous fat preference, and digestive secretions.", "J. Clin. Invest.", "2005", "Febbraio M., Besnard P., Niot I., Laugerette F., Montmayeur J.P., Passilly-Degrace P., Patris B.", "protein_xref_pubmed", "16276419", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "FAT/CD36: a major regulator of neuronal fatty acid sensing and energy homeostasis in rats and mice.", "Diabetes", "2013", "Dunn-Meynell A., Le Foll C., Levin B.E., Magnan C., Musatov S.", "protein_xref_pubmed", "23557700", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Fatty acid translocase/CD36 mediates the uptake of palmitate by type II pneumocytes.", "Am. J. Physiol.", "1999", "Spener F., Haupt R., Guthmann F., Looman A.C., Ruestow B.", "protein_xref_pubmed", "10409247", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Purification of the major substrate for palmitoylation in rat adipocytes: N-terminal homology with CD36 and evidence for cell surface acylation.", "J. Lipid Res.", "1993", "Hays J., Jochen A.", "protein_xref_pubmed", "7504047", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Cloning of a rat adipocyte membrane protein implicated in binding or transport of long-chain fatty acids that is induced during preadipocyte differentiation. Homology with human CD36.", "J. Biol. Chem.", "1993", "El-Maghrabi M.R., Lopez E., Abumrad N.A., Amri E.-Z., Grimaldi P.A.", "protein_xref_pubmed", "7688729", "protein_xref_uniprotkb", "Q07969" ], [ "Q07969-1", "Binding of sulfosuccinimidyl fatty acids to adipocyte membrane proteins: isolation and amino-terminal sequence of an 88-kD protein implicated in transport of long-chain fatty acids.", "J. Membr. Biol.", "1993", "Abumrad N.A., Harmon C.M.", "protein_xref_pubmed", "8320718", "protein_xref_uniprotkb", "Q07969" ], [ "A0A096MJY4-1", "MEF2C DNA-binding activity is inhibited through its interaction with the regulatory protein Ki-1/57.", "FEBS Lett.", "2005", "Kobarg J., Crosara-Alberto D.P., Franchini K.G., Kobarg C.B., Theizen T.H.", "protein_xref_pubmed", "15862299", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A096MJY4-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A096MJY4" ], [ "A0A0G2KA92-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "A0A096MJY0" ], [ "Q62949-1", "A cortical neuropeptide with neuronal depressant and sleep-modulating properties.", "Nature", "1996", "Danielson P.E., Sutcliffe J.G., de Lecea L., Henriksen S.J., Gautvik K.M., Criado J.R., Dunlop C.L.M., Prospero-Garcia O., Schweitzer P., Siggins G.R.", "protein_xref_pubmed", "8622767", "protein_xref_uniprotkb", "Q62949" ], [ "P01946-1", "Molecular cloning and characterization of two sets of alpha-theta genes in the rat alpha-like globin gene cluster.", "Gene", "1999", "Sato H., Okazaki T., Satoh H., Nagae Y., Inokuchi N.", "protein_xref_pubmed", "10196478", "protein_xref_uniprotkb", "P01946" ], [ "P01946-1", "The amino acid sequence of the alpha chain of the major haemoglobin of the rat (Rattus norvegicus).", "Biochem. 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Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "P09006" ], [ "D4A781-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "M0RB74" ], [ "Q9JHY8-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q9JHY8" ], [ "Q9JHY1-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q9JHY1" ], [ "Q02874-1", "Structural characterization of the histone variant macroH2A.", "Mol. Cell. Biol.", "2005", "Luger K., Pehrson J.R., Chakravarthy S., Khochbin S., Caron C., Gundimella S.K., Perche P.-Y.", "protein_xref_pubmed", "16107708", "protein_xref_uniprotkb", "Q02874" ], [ "Q02874-1", "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues.", "Nat. Commun.", "2012", "Olsen J.V., Lage K., Secher A., Dmytriyev A., Lundby A., Lundby C., Nordsborg N.B.", "protein_xref_pubmed", "22673903", "protein_xref_uniprotkb", "Q02874" ], [ "Q02874-1", "MacroH2A, a core histone containing a large nonhistone region.", "Science", "1992", "Fried V.A., Pehrson J.R.", "protein_xref_pubmed", "1529340", "protein_xref_uniprotkb", "Q02874" ], [ "Q02874-1", "Developmental and tissue expression patterns of histone macroH2A1 subtypes.", "J. Cell. Biochem.", "1997", "Pehrson J.R., Costanzi C., Dharia C.", "protein_xref_pubmed", "9138085", "protein_xref_uniprotkb", "Q02874" ], [ "Q05474-1", "The carboxyl extension of a ubiquitin-like protein is rat ribosomal protein S30.", "J. Biol. Chem.", "1993", "Olvera J., Wool I.G.", "protein_xref_pubmed", "8394356", "protein_xref_uniprotkb", "Q05474" ], [ "Q99JD4-1", "Clasps are CLIP-115 and -170 associating proteins involved in the regional regulation of microtubule dynamics in motile fibroblasts.", "Cell", "2001", "Akhmanova A., Hoogenraad C.C., Galjart N., Grosveld F., Stepanova T., Vermeulen W., Burgering B.M., Dortland B., Drabek K., Verkerk T., de Zeeuw C.I.", "protein_xref_pubmed", "11290329", "protein_xref_uniprotkb", "Q99JD4" ] ] }, "readme": "Name\n - Rat Protein Citations (UniProtKB)\n\nVersion\n - 1.11.2\n\nCreated on\n - 2019-09-06T14:06:38.980261\n\nModified on\n - 2022-01-19T13:23:57.978155\n\nCreated by\n - Jeet Vora [jeetvora@gwu.edu], Rahi Navelkar [rsn13@gwu.edu], Robel Kahsay [rykahsay@gwu.edu], Xavier Holmes [xavierh@email.gwu.edu], Karina Martinez [karinamartinez@gwu.edu], Amanda Bell [amandab2140@gwu.edu], Jonathon Keeney [keeneyjg@gwu.edu], Millicent Quartey [mquartey@email.gwu.edu]\n\nAuthors\n - Maria Martin [martin@ebi.ac.uk], Preethi Vasudev [pvasudev@ebi.ac.uk]\n\nChecksum\n - \n\nUsability Domain\n - The Rat Protein Citations dataset contains publication information for rat [taxid:10116] UniProtKB accessions that includes PMID, journal name, date and author and title. Publications of large scale studies, and high frequency publications pertaining to genome sequencing, cDNA, chromosomes have been filtered out as per https://data.glygen.org/ln2wwwdata/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv. The dataset is derived from 2019-09 UniProtKB release. If you use this dataset please provide proper attribution to EMBL-EBI-UniProtKB and GlyGen. \n\nDescription Domain\n Keywords\n - publications\n - PMID\n - journal\n - citations\n - authors\n - UniProtKB\n - PubMed\n\n Pipeline Steps\n - Step-1: The script loads the UniProtKB publication data from the triplestore containing triples from nt file to retrieve the publication information associated with the UniProtKB accession and maps it to the UniProtKB canonical accessions. The script also filters out publications of large scale studies, and high frequency publications pertaining to DNA sequencing, cDNA, chromosomes using blacklisted PMIDs file. \n\nExecution Domain\n Scripts - https://github.com/GW-HIVE/glygen-backend-integration/blob/master/pipeline/integrator/make-protein-dataset.py\n\n\n Software Prerequisites\n Name: Python\n Version: 2.7.5\n URI: https://www.python.org/download/releases/2.7.5/\n\nI/O Domain\n Input Subdomain\n Name: uniprot-proteome-rattus-norvegicus.nt\n URI: https://data.glygen.org/ln2wwwdata/source/uniprot-proteome-rattus-norvegicus.nt\n Name: rat_protein_masterlist.csv\n URI: https://data.glygen.org/ln2wwwdata/reviewed/rat_protein_masterlist.csv\n Name: rat_protein_blacklisted_pmids_uniprotkb.csv\n URI: https://data.glygen.org/ln2wwwdata/compiled/rat_protein_blacklisted_pmids_uniprotkb.csv\n Output Subdomain\n Name: rat_protein_citations_uniprotkb.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_protein_citations_uniprotkb.csv\n Name: rat_protein_citations_uniprotkb.stat.csv\n URI: http://data.glygen.org/ln2wwwdata/reviewed/rat_protein_citations_uniprotkb.stat.csv\n\nFields\n Name: \"uniprotkb_canonical_ac\"\n Description: \"\"\n Unique Values: \"16\"\n Name: \"motif_start\"\n Description: \"\"\n Unique Values: \"23\"\n Name: \"filter_flags\"\n Description: \"Filter tags/flags assigned to the mutation entries that have passed the mutation filter criteria\"\n Unique Values: \"19\"\n Name: \"sift_prediction\"\n Description: \"The SIFT qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"3\"\n Name: \"somatic_status\"\n Description: \"The status of the variant whether it is germline (somatic status =0) or somatic (somatic status =1) variant\"\n Unique Values: \"1\"\n Name: \"chr_pos\"\n Description: \"Chromosome Position of a gene\"\n Unique Values: \"19\"\n Name: \"chr_id\"\n Description: \"\"\n Unique Values: \"10\"\n Name: \"dbsnp_id\"\n Description: \"\"A reference SNP ID number\"\n Unique Values: \"19\"\n Name: \"evidence_ECO:0000313\"\n Description: \"A type of evidence that is imported information used in an automatic assertion\"\n Unique Values: \"1\"\n Name: \"xref_id\"\n Description: \"ID of the X-ref\"\n Unique Values: \"19\"\n Name: \"mim_id\"\n Description: \"Disease ID from the OMIM database\"\n Unique Values: \"1\"\n Name: \"description\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"begin_aa_pos\"\n Description: \"Start position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"cytogenic_band\"\n Description: \"One of the subregions of a chromosome visible microscopically after special staining\"\n Unique Values: \"14\"\n Name: \"aa_pos\"\n Description: \"Position of the amino acid in canonical sequence of protein in the UniProtKB database\"\n Unique Values: \"18\"\n Name: \"ref_aa\"\n Description: \"Reference amino acid residue\"\n Unique Values: \"9\"\n Name: \"sift_score\"\n Description: \"SIFT predicts whether an amino acid substitution is likely to affect protein function based on sequence homology and the physico-chemical similarity between the alternate amino acids. The data we provide for each amino acid substitution is a score and a qualitative prediction (either 'tolerated' or 'deleterious'). The score is the normalized probability that the amino acid change is tolerated so scores nearer zero are more likely to be deleterious. The qualitative prediction is derived from this score such that substitutions with a score < 0.05 are called 'deleterious' and all others are called 'tolerated\"\n Unique Values: \"10\"\n Name: \"alt_motif\"\n Description: \"Altered motif\"\n Unique Values: \"24\"\n Name: \"disease_xrefs\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"polyphen_score\"\n Description: \"The score assigned to a amino acid substitution by a tool called as PolyPhen (=Polymorphism Phenotyping) which predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. The PolyPhen score ranges from 0.0 (tolerated) to 1.0 (deleterious). Variants with scores of 0.0 are predicted to be benign. Values closer to 1.0 are more confidently predicted to be deleterious\"\n Unique Values: \"1\"\n Name: \"polyphen_prediction\"\n Description: \"\"The PolyPhen prediction values are - greater than 0.908 - \"\"Probably Damaging\"\"; greater than 0.446 and less than or equal to 0.908 - \"\"Possibly Damaging\"\"; less than or equal to 0.446 - \"\"Benign\"\"\"\n Unique Values: \"1\"\n Name: \"is_known_glycoprotein\"\n Description: \"Yes or no flag to denote if a protein is experimentally proven glycoprotein\"\n Unique Values: \"1\"\n Name: \"alt_nt\"\n Description: \"Alternative nucleotide\"\n Unique Values: \"1\"\n Name: \"protein_name\"\n Description: \"Protein name in the UniProtKB\"\n Unique Values: \"16\"\n Name: \"disease_evidence_ECO:0000313\"\n Description: \"The evidence that could be a PMID or a ClinVar ID that associates disease with the variant\"\n Unique Values: \"1\"\n Name: \"effect\"\n Description: \"The effect on glycosylation or N-sequon due to variation at site of glycosylated amino acid.\"\n Unique Values: \"3\"\n Name: \"end_aa_pos\"\n Description: \"End position of the amino acid in the sequence of a protein in UniProtKB\"\n Unique Values: \"18\"\n Name: \"mutation_type\"\n Description: \"Denotes whether mutation was reported with reference to amino acid or nucleotide\"\n Unique Values: \"1\"\n Name: \"disease_description\"\n Description: \"The disease description and/or definition \"\n Unique Values: \"1\"\n Name: \"do_id\"\n Description: \"Disease Ontology identifier\"\n Unique Values: \"1\"\n Name: \"evidence_ECO:0000269\"\n Description: \"A type of experimental evidence that is used in a manual assertion. Usually the values are PMIDs\"\n Unique Values: \"1\"\n Name: \"ref_nt\"\n Description: \"Reference nucleotide\"\n Unique Values: \"4\"\n Name: \"disease\"\n Description: \"The disease name for the cell line\"\n Unique Values: \"1\"\n Name: \"alt_aa\"\n Description: \"Altered amino acid residue\"\n Unique Values: \"10\"\n Name: \"cosmic_id\"\n Description: \"Legacy mutation identifier (COSM) in Catalogue of Somatic Mutations in Cancer (COSMIC) represents existing COSM mutation identifiers. This identifier remains the same between different assemblies (GRCh37 and GRCh38). All the COSM ids at the same genomic location have been collapsed into one representative COSM id. These ids are maintained to help track existing mutations\"\n Unique Values: \"1\"\n Name: \"ref_motif\"\n Description: \"Reference motif\"\n Unique Values: \"20\"\n Name: \"xref_key\"\n Description: \"Source key associated to the xref_id\"\n Unique Values: \"2\"\n Name: \"minor_allelic_frequency\"\n Description: \"\"\n Unique Values: \"1\"\n Name: \"gene_name\"\n Description: \"\"Official gene name/symbol assigned to the gene. Human gene name/symbol are approved by the HUGO Gene Nomenclature Committee (HGNC) and mouse gene name are approved by the Mouse Genome Informatics (MGI)\"\n Unique Values: \"17\"\n Name: \"disease_evidence_ECO:0000269\"\n Description: \"The PMID evidence for the association of the disease with the variant.\"\n Unique Values: \"1\"", "downloadurl": "/ln2data/releases/data/v-1.11.2/reviewed/rat_protein_citations_uniprotkb.csv" }